Open Biomedical Ontologies Open Biomedical Ontologies OBO n

Open Biomedical Ontologies

Open Biomedical Ontologies (OBO) n An umbrella project for grouping different ontologies in biological/medical field – a repository for ontologies with defined set of standards n Available from a single source: http: //obo. sourceforge. net/

Why do we need OBO? n GO covers three domains of biology: – molecular function of a protein – biological function of a protein – cellular location of a protein

Why do we need OBO? n Lots of other aspects could also be annotated, e. g. : – phenotype – anatomy – genomic – taxonomy

Why do we need OBO? n Other groups outside of GO developed own ontologies for their own use – e. g. anatomies for specific organisms n No standardisation of ontologies with respect to: – format – scope – relationships No way of knowing whether such ontologies already exist n No mechanism of distribution for other groups n

Why do we need OBO? n Creating ontologies takes a lot of work – Makes sense to reuse existing ontologies where possible n Improves data integration where small set of ontologies used n Allows ontologies to be made available from a single place

Why do we need OBO? n In addition, GO also contains other ‘implicit’ ontologies: – anatomies • e. g. eye development – chemical • e. g. silicone metabolism – cell type • e. g. erythrocyte differentiation

Why do we need OBO? n Useful to have the implicit ontologies – can be ‘aligned’ with GO – Helps highlight errors – For reasoning (advanced GO!)

OBO requirements To be part of OBO, ontologies must: n Be open, can be used by all without any constraint

OBO requirements: open n Ontologies can be used by anyone without any constraints, except: – original authors are acknowledged – cannot be edited and then released under same name

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint n Be in a common shared syntax n

OBO requirements: syntax n Usually the OBO format, same as primary GO format – and adaptions of OBO format Also accept OWL (Web Ontology Language) format n Allows the same tools to be applied, facilitating shared software implementations n

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint n Be in a common shared syntax n Not overlap with other ontologies in OBO n

OBO requirements: overlapping n Ontologies can overlap partially, but large overlap should be avoided n Idea is that terms from different ontologies can be combined to form new terms n Striving for accepted standards rather than competition

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint n Be in a common shared syntax n Not overlap with other ontologies in OBO n Share a unique identifier space n

OBO requirements: id space n So, for example, the GO identifier is GO: – No other OBO ontology could use this id space n Prevents problems where ontologies are used together

OBO requirements To be part of OBO, ontologies must: n n n Be open, can be used by all without any constraint Be in a common shared syntax Not overlap with other ontologies in OBO Share a unique identifier space Include text definitions of their terms

OBO requirements n In addition, OBO includes ontology of relationships – all ontologies should use these definitions of relationships n For example – part_of – develops_from – regulates

What’s available n demo: http: //obo. sourceforge. net/

How you might use OBO n Extra annotation – developmental timelines – taxonomy – pheontype n Create your own ontologies and submit to OBO – e. g. anatomy of your organism